People normally use Nexus Copy Number to analyze their own data for copy number events and are mesmerized by its many powerful yet easy-to-use functions. However, most of the users ignore a hidden gem in the software and are really missing out on a beautiful thing.
The hidden gem is Nexus DB, which is on the starting window when the software is launched. Nexus DB is an Amazon cloud (AWS) based repository for Nexus projects and users can sign up free login accounts inside the Nexus software to access it.
Initially designed for data sharing via the cloud, Nexus DB allows Nexus users to upload and download Nexus projects. This enables data sharing for collaborations among research groups anywhere in the world. But the most valuable thing is the existing Nexus projects already in Nexus DB, which include lots of public data sets from GEO and TCGA. TCGA (The Cancer Genome Atlas) has terabytes of data from over 30 different tumor types that contain copy number data from SNP arrays, sequence variants data from whole exome sequencing (WES), and gene expression data from RNA-seq. Downloading and storing such huge data sets is always a challenge for individual researchers. With Nexus DB, the seemingly impossible task is just a couple of mouse clicks.
And most important, we have curated all of the TCGA Level 1 data (raw data) with the best analyzing settings and ploidy adjusments, and stored them in Nexus DB for researchers to get the most trustable results with the best data quality, which has been the biggest issue for the TCGA Level 3 data (processed data on TCGA website). These are the TCGA Premier data sets.
Download a TCGA Premier data set and click the View button, the copy number events and their related sequence variants (somatic mutations) are available for visualization. With the powerful statistical functions in Nexus Copy Number, downstream analyses like GISTIC, clustering, group comparisons, survival analysis, can then be easily carried out.